RFdiffusion3 Documentation

RFdiffusion3 is a powerful protein design tool that operates on the atomic level to study ligand-protein interactions, create nucleic acid-protein interfaces, and design de novo enzymes. It is designed to be highly flexible and user-friendly, making it suitable for a wide range of applications in computational biology and biochemistry.

New to RFD3?

If you haven’t installed RFD3 yet, take a look at the RFD3 README or, if you are on a UNIX system, see the Installation of RFdiffusion3 on Unix Systems .

Once you have everything installed, check out one of our Introductory Tutorials, listed below.

General

• Installation of RFdiffusion3 on Unix Systems
• Inference Calculation Basics
• RFdiffusion3 — Input Specification & Command-line arguments
• RFD3 inference acceleration
• RFdiffusion3 — Output Metrics
• Common Issues

RFD3 Design Tips

• Designability vs. Diversity
• Tips for Designing Enzymes with RFdiffusion3

Introductory Tutorials

These introductory tutorials are designed to help users get familiar with the capabilities of RFD3 for specific design tasks.

• Protein-Protein Interface Design in RFdiffusion3
• Enzyme Design in RFdiffusion3
• Nuclei Acid Binder Design in RFdiffusion3

Intermediate Tutorials

These intermediate tutorials cover more complex topics related to specific design tasks in RFD3. If this is your first time using RFD3, we recommend starting with the introductory tutorials before moving on to these.

• Intermediate Enzyme Design Tutorial
• Protein and Small Molecule Binder Design with Hydrogen Bond Conditioning

Advanced Tutorials

The advanced RFdiffusion3 tutorials focus on more complex design tasks and provide in-depth explanations of the underlying principles and techniques used in RFD3. These tutorials assume some knowledge of the use of PyMOL (or other visualization software) and basic RFdiffusion3 concepts that are described in the introductory and intermediate tutorials.

• Advanced Enzyme Design with RFdiffusion3

Examples

The following examples demonstrate how to use RFD3 for various design tasks. However, they do not go into detail about how to set up RFD3 or how the different constraints work. If you are new to RFD3, we recommend starting with the introductory tutorials before moving on to these examples.

• RFdiffusion3 — Nucleic acid binder design examples
• RFdiffusion3 — Small molecule binder design examples
• RFdiffusion3 — Protein binder design examples
• N-to-C macrocycle design
• Overview of Symmetry in RFD3
• RFdiffusion3 — Enzyme design examples